X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=0946396e3a0fe6623f3501feed5fc6e7b4ba239a;hb=2397df97b12cd5d21ea10dc4248c18a5803ddd41;hp=17f1b3387ee1279a3b44e6ef3d34b732fc88834d;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 17f1b33..0946396 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,31 +11,28 @@
  */
 
 #include "command.hpp"
-#include "globaldata.hpp"
-#include "sequence.hpp"
+#include "filters.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-	FilterSeqsCommand();
+	FilterSeqsCommand(string);
 	~FilterSeqsCommand() {};
 	int execute();	
+	void help();
 	
 private:
-	void doHard();
-	void doTrump(Sequence);
-	void doVertical();
-	void doSoft();
-	void getFreqs(Sequence);
-	string filter;	
+	string vertical, filter, fastafile, hard, outputDir;	
 	int alignmentLength;
 
 	char trump;
-	bool vertical;
+	bool abort;
 	float soft;
 	int numSeqs;
 	
-	GlobalData* globaldata;	
+	Filters F;
+		
 	vector<int> a, t, g, c, gap;
 
 };